rs781301028
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_001130823.3(DNMT1):c.4483G>A(p.Val1495Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000918 in 1,611,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001130823.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMT1 | NM_001130823.3 | c.4483G>A | p.Val1495Met | missense_variant | 37/41 | ENST00000359526.9 | NP_001124295.1 | |
DNMT1 | NM_001318730.2 | c.4435G>A | p.Val1479Met | missense_variant | 36/40 | NP_001305659.1 | ||
DNMT1 | NM_001379.4 | c.4435G>A | p.Val1479Met | missense_variant | 36/40 | NP_001370.1 | ||
DNMT1 | NM_001318731.2 | c.4120G>A | p.Val1374Met | missense_variant | 37/41 | NP_001305660.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNMT1 | ENST00000359526.9 | c.4483G>A | p.Val1495Met | missense_variant | 37/41 | 1 | NM_001130823.3 | ENSP00000352516.3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000449 AC: 11AN: 244814Hom.: 0 AF XY: 0.0000677 AC XY: 9AN XY: 132900
GnomAD4 exome AF: 0.0000952 AC: 139AN: 1459660Hom.: 0 Cov.: 32 AF XY: 0.000103 AC XY: 75AN XY: 725960
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74376
ClinVar
Submissions by phenotype
Hereditary sensory neuropathy-deafness-dementia syndrome;C3807295:Autosomal dominant cerebellar ataxia, deafness and narcolepsy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 05, 2021 | - - |
Hereditary sensory neuropathy-deafness-dementia syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at